Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.
Mol Biol Evol. 2024 Nov 1;41(11). doi: 10.1093/molbev/msae212.
Previous studies revealed extensive genetic introgression between Ovis species, which affects genetic adaptation and morphological traits. However, the exact evolutionary scenarios underlying the hybridization between sheep and allopatric wild relatives remain unknown. To address this problem, we here integrate the reference genomes of several ovine and caprine species: domestic sheep, argali, bighorn sheep, snow sheep, and domestic goats. Additionally, we use 856 whole genomes representing 169 domestic sheep populations and their six wild relatives: Asiatic mouflon, urial, argali, snow sheep, thinhorn sheep, and bighorn sheep. We implement a comprehensive set of analyses to test introgression among these species. We infer that the argali lineage originated ∼3.08 to 3.35 Mya and hybridized with the ancestor of Pachyceriforms (e.g. bighorn sheep and snow sheep) at ∼1.56 Mya. Previous studies showed apparent introgression from North American Pachyceriforms into the Bashibai sheep, a Chinese native sheep breed, despite of their wide geographic separation. We show here that, in fact, the apparent introgression from the Pachyceriforms into Bashibai can be explained by the old introgression from Pachyceriforms into argali and subsequent recent introgression from argali into Bashibai. Our results illustrate the challenges of estimating complex introgression histories and provide an example of how indirect and direct introgression can be distinguished.
先前的研究揭示了绵羊属物种之间广泛的遗传渗入，这影响了遗传适应和形态特征。然而，绵羊与异域野生物种杂交的具体进化情景仍然未知。为了解决这个问题，我们整合了几种绵羊和山羊物种的参考基因组：家绵羊、盘羊、大角羊、雪羊和家山羊。此外，我们使用了代表 169 个家绵羊种群及其六个野生亲缘种的 856 个全基因组：亚洲摩弗伦羊、野山羊、盘羊、雪羊、捻角山羊和大角羊。我们进行了一系列综合分析来检验这些物种之间的基因渗入。我们推断盘羊谱系起源于约 3.08 至 3.35 百万年前，并在约 1.56 百万年前与 Pachyceriforms 的祖先（如大角羊和雪羊）杂交。先前的研究表明，尽管北美 Pachyceriforms 和 Bashibai 绵羊（中国本土绵羊品种）在地理上相隔很远，但存在明显的基因渗入。我们在这里表明，实际上，从北美 Pachyceriforms 到 Bashibai 的明显基因渗入可以用 Pachyceriforms 到盘羊的古老基因渗入以及随后盘羊到 Bashibai 的近期基因渗入来解释。我们的结果说明了估计复杂基因渗入历史的挑战，并提供了一个如何区分间接和直接基因渗入的例子。
